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Re: SNP annotation in R

Valerie Obenchain — 2013-06-18T22:11:51

Hi Ina,

It looks like the chromosome names in 'target' don't match those in the 
TranscriptDb. There is an example on the locateVariants man page of how 
to inspect the seqlevels (chromosome names) with seqlevels() and change 
them with renameSeqlevels().

Once you've made the change, confirm that the names match with the 
intersect() function. This is also demonstrated on the man page.

Valerie

On 06/18/2013 01:47 PM, Ina Hoeschele wrote:

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SNP annotation in R

Ina Hoeschele — 2013-06-18T20:47:25

Hi,
  I am interested in annotating lists of SNPs in R, mostly I am interested in finding the gene a SNP is located in and for intergenic SNPs which genes are close by. I found this code that wsa developed with the help of Valerie Obenchain:
http://adairama.wordpress.com/2013/02/15/functionally-annotate-snps-and-indels-in-bioconductor/
However, when I adapted this code to my problem I got the error message below. Can someone please give me a hint?
Thanks, Ina

input <- SNP.map.retain[SNPs,1:3]
rownames(input) <- NULL
colnames(input) <- c("rsid", "chr", "pos")
input
#       rsid chr      pos
#1  rs661761   1 30618672
#2 rs3754508   1 17255474
#3 rs6426403   1  4169394
#4  rs228727   1  7770423
#5 rs1635592   1 17535994
target <- with(input,
                GRanges( seqnames = Rle(chr),
                         ranges   = IRanges(pos, end=pos, names=rsid),
                         strand   = Rle(strand("*")) ) )
target
#GRanges with 5 ranges and 0 metadata columns:
#            seqnames               ranges st

Re: makePdInfoPackage for Primeview arrays

cstrato — 2013-06-18T19:18:09

Dear Max,

In principle you could also use package xps, which can handle PrimeView 
arrays. To create a root 'scheme' file (see vignette xps.pdf) you simply 
need to do:

### new R session: load library xps
library(xps)

### define directories:
# directory containing Affymetrix library files
libdir <- "/Volumes/GigaDrive/Affy/libraryfiles"
# directory containing Affymetrix annotation files
anndir <- "/Volumes/GigaDrive/Affy/Annotation"
# directory to store ROOT scheme files
scmdir <- "/Volumes/GigaDrive/CRAN/Workspaces/Schemes"

### create scheme file:
scheme.primeview <- import.expr.scheme("primeview", filedir = 
file.path(scmdir, "na33"),
                          schemefile = file.path(libdir, "PrimeView.CDF"),
                          probefile  = file.path(libdir, 
"PrimeView.probe.tab"),
                          annotfile  = file.path(anndir, "Version12Nov", 
"PrimeView.na33.annot.csv"))

For more information and examples see also the example scripts in 
xps/examples/script4schemes.R and xps/examples

Re: What is a good "control" for bacteria RNA-seq samples from a series of time points

Simon Anders — 2013-06-18T18:31:09

Hi Nancy

On 18/06/13 20:24, Yanxiang Shi wrote:

How would this help? As the untreated cells will not slow down in their 
growth, the "untreated at time T" sample will be as badly matched for 
cell density as the "untreated at time 0" sample.

Or do you want to manually dilute the untreated time-course to mimic the 
density changes?

   Simon

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Re: What is a good "control" for bacteria RNA-seq samples from a series of time points

Yanxiang Shi — 2013-06-18T18:24:59

Hi Sam,

Thank you for your reply! My only concern is my cells stopped growing /
slow down after the treatment, so that the cell densities at certain time
point are different between control and treated cells, while the time
density at time points can be similar as Time zero. Thus I am worried some
pathways that are controlled related to cell density will be transcribed
differently. So should I have two controls: "a time zero no treatment" and
"time point no treatment"?

Thank you for your opinion!

Best,
Nancy


On Fri, Jun 14, 2013 at 11:47 PM, Sam McInturf <smcinturf-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:


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Re: makePdInfoPackage for Primeview arrays

Benilton Carvalho — 2013-06-18T18:05:52

Unfortunately, I cannot provide a quick fix for this. The reason is
that pdInfoBuilder, for expression arrays, relies on the fact that one
probe belongs to only one probeset. And this is not true for primeview
chips.

For example, the probe with chip coordinates X=135 and Y=147 is shared
by two probesets (11715100_at and 11715102_x_at)... and this happens
for thousands of other probesets.

Before changing the code, I want to make sure I fully understand the
background for this chip and why duplicity happens... and this may
take a while...

Will get back to the list once I have news on this front,

b

2013/6/18 Max Kauer <maximilian.kauer-NsU1hilb7eQ< at >public.gmane.org>:

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makePdInfoPackage for Primeview arrays

Max Kauer — 2013-06-18T13:25:11

Hi,

I am trying to make a pd.info package for the Affy Primeview array, but I
get an error.

Thanks for any help!

Cheers,

Max

 

 

This is my code:

 

library(pdInfoBuilder)

cdf <- list.files( pathAnnotPr, pattern = ".cdf", full.names = TRUE )

cel <- list.files( pathC, pattern = ".CEL", full.names = TRUE )[1] #  take
first array

tab <- list.files(pathAnnotPr, pattern = "_tab", full.names = TRUE)

 

seed <- new("AffyExpressionPDInfoPkgSeed",

      cdfFile = cdf, celFile = cel,

      tabSeqFile = tab, author = "xx",

      email = "xx",

      biocViews = "AnnotationData",

      genomebuild = "hg19",

      organism = "Human", species = "Homo Sapiens",

      url = "xx"

)

makePdInfoPackage( seed, destDir = "." )

 

 

 

Which produces this output/error (although a pd.primeview directory is
created):

 

============================================================================
====

Building annotation package for Affymetrix Expression array

CDF...............:  PrimeView.cdf 

CEL.........

Re: Finding the common ID from 3 objects or excels files in R

Sean Davis — 2013-06-18T13:14:47

See the match() function.

Sean


2013/6/18 Nikul Soni <soninikul007< at >gmail.com>:
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Finding the common ID from 3 objects or excels files in R

Nikul Soni — 2013-06-18T12:27:08

Dear all,

i have three excel files and also saved as object and  i am trying to
extract common genes sorted according to the ID in R .

Can anyone help me how to do it.

Thanks
Nikul

Re: DESeq2 with multiple groups

Michael Love — 2013-06-18T12:05:15

hi Lorena,

On Tue, Jun 18, 2013 at 1:40 PM, Lorena Pantano
<lorena.pantano-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote:

Yes, you can use a design formula like you have written to control for
sex and population, and then retrieve the results for only the
'condition' variable. Better would be to put 'condition' at the end of
the design, so that it is the default variable used by results() and
plotMA(). The results function has an argument 'name', which specifies
which variable+factor-level which should be used for constructing the
results DataFrame. By default, the last factor level of the last
variable is used. This is discussed in the vignette and in the man
page for results().

The resultsNames() function will return the possible names which you
can supply to the 'name' argument of results():

resultsNames(dds)

-Mike

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Re: DESeq2 with multiple groups

Lorena Pantano — 2013-06-18T11:40:10

I am using your package (which is great!) but I have a question.

I have a table with individuals that have two more groups beside the
condition column: like sex and population. Could I put as formula ~
conditions +sex +population, and when I retrieve the results from
Condition, will I get only DE genes that are due to the condition and not
due to sex or population?

cheers

Lo


On Tue, Jun 18, 2013 at 1:34 PM, Michael Love
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Re: diffbind, paired end reads

Gordon Brown — 2013-06-18T08:51:40

Hi, Rory, Kasper,

DiffBind's original counting code treats paired-end data the same as
single-end, i.e. each read is considered separately, with no attention
paid to whether it's part of a pair.  As long as all the libraries are the
same (all S.E. or all P.E.) it shouldn't affect the outcome; counts will
just be double for P.E. cases (disregarding improperly paired reads).

To fix it properly, since we accept bed as well as bam, we'd have to test
for properly paired reads ourselves, possibly doing it just that bit
differently from other tools.  Personally, I'd rather not open that box...

Cheers,

 - Gord


On 2013-06-17 23:55, "Rory Stark" <Rory.Stark-qkclRPqtJ+fQzY9nttDBhA< at >public.gmane.org> wrote:


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DEXSeq Question <|------Ignore, I figured it out.

Margaret Linan — 2013-06-18T06:43:11


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ReportingTools: formatting html report

Gabriel Becker — 2013-06-18T05:53:02

Abhi,

Great to hear from someone using ReportingTools "in the wild". I'm glad you
are finding it useful.

I only see two requests in your message, though you mentioned having 3.

I will answer the one about images first. It is entirely possible to have
multiple images per row. The "adding plots or links to a report table"
section of the basic ReportingTools vignette describes how to add or
customize columns within a table, including columns whose contents are
images. Having multiple images per row is as simple as adding multiple
image columns to the table.

As for aligning the entire report, formal support for custom CSS is a
feature which we hope to have in the next version of ReportingTools, but
didn't make it into this one. That said, you have both full control over
the publishing methods and direct access to the DOM so I believe there are
various things you can do to override the alignment of a specific table (or
all tables, etc) with the current version.

I'm not on a computer that has ReportingTools i

Re: ReportingTools: formatting html report

Jason Hackney — 2013-06-18T04:34:16

Hi Abhi,

I'm glad that you've gotten RpeortingTools working. Perhaps Josh can
discuss a bit how to customize the alignment and spacing of the tables that
are produced. I'm much less familiar with the CSS options that exist.

For your second question, we can look to the examples in the microarray
analysis vignette for some hints about how to do this. In the "Differential
expression analysis using limma" section, there's a function for producing
one plot per row in the table. We can extend this example like this:

+         imagenames1 <- paste0(df$ProbeId, "_1")
+         imagenames2 <- paste0(df$ProbeId, "_2")
+         imagenames3 <- paste0(df$ProbeId, "_3")
+         for (i in 1:nrow(df)){
+                 probeId <- df$ProbeId[i]
+                 pl1 <- xyplot(...)
+                 pl2 <- xyplot(...)
+                 pl3 <- xyplot(...)
+                 png(filename = paste0("./reports/figuresde_analysis/",
+                       imagenames1[i]))
+                 print(pl1)
+                 dev.of

DEXSeq Question

Margaret Linan — 2013-06-18T03:06:14

Dear Simon, Alejandro, etc

I am trying to get the associated gene name printed next to the gene id
column that is displayed on the HTML report created by the DEXSeqHTML
function.

I am aware there are options within the function, but I do not know how to
use them to get the result that I am looking for.
For example I do not know how to create a mart class object or use the
attributes option.

I have tried to google all of my concerns but haven't found a good example
or explanation yet.

Please help?

Thanks,
Margaret Linan

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number of variable in svm plot

nofe [guest] — 2013-06-17T23:50:34

hi all,

the data set i have consists of

x which is a matrix of 39 cancer patients [rows] and 2000 gene names [colmns]. each cell is the value of the gene for a particular patient. there are two types of cancer people  representedas factor y.


here is the code:

library(e1071)

#load database

 db <- read.csv(file="databases\\colon-cancer\\colon-cancer.csv",head=FALSE,sep=",") 

x = as.matrix(db[,1:(ncol(db)-1)])
  y = as.factor(db[,ncol(db)])

  svmModel = svm(x, y, cost = 10, cachesize=500,  scale=F,
  type="C-classification", kernel="linear" )

my question is :to plot the svm model i need to plot 2 vaiables as y axis and x axis....but according to the nature of my dataset i have about 2000 variables?? does that mean i have to plot only two?? or is there a way to plot all of the 2000 and beable to show how the svm model classify the dataset. 

 -- output of sessionInfo(): 

sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Arabic_Saudi Arabia.12

Re: diffbind, paired end reads

Rory Stark — 2013-06-17T22:55:44

Hi Kasper-





Gord, how does the default count code handle paired-end data (in pre-1.6 DiffBind, or when bLowMem=FALSE)?

Cheers-
Rory

________________________________
From: Kasper Daniel Hansen [kasperdanielhansen-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org]
Sent: 17 June 2013 21:51
To: Rory Stark
Subject: diffbind, paired end reads

Hi Rory

Just skimming DiffBind.  I was surprised there is not a longer discussion of dba.count() in the vignette regarding supported input formats.  I also read (skimmed) the man pages.  It is not clear to me if DiffBind supports paired end reads in the counting step (and also how it deals with for example a paired end read where only one mate aligns).

Hope all is well in Cambridge.

Best,
Kasper

NOTICE AND DISCLAIMER
This e-mail (including any attachments) is intended for ...{{dropped:20}}

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ReportingTools: formatting html report

Abhishek Pratap — 2013-06-17T22:45:33

Hi Guys

Now that I am able to create basic reports which already are a great
time saver. I am wondering do I have some flexibility to decide where
to render images and some page formatting options.

For example I have three specific requirements at this point.

1. Left align the whole page. Currently a rendered table is centered
cutting the displayed text as it is horizontally broad

2. put multiple images in a single row; in other words put 2-3 images
side by side in a row.


Thanks!
-Abhi

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Re: Missing as.list generic from AnnotationDbi?

Ryan C. Thompson — 2013-06-17T22:43:31

Never mind, reinstalling the AnnotationDbi package seems to have solved 
the problem. No idea what was wrong.

On Mon 17 Jun 2013 03:23:54 PM PDT, Ryan C. Thompson wrote:

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Re: help with ReportingTools

Abhishek Pratap — 2013-06-17T22:39:44

Just for completeness...after updating to the latest versions it works well.

I now have other specific questions with regards to page formatting
with ReportingTools. I will start another specific thread for the
same.

Cheers!
-Abhi

On Mon, Jun 17, 2013 at 10:37 AM, Abhishek Pratap <apratap-/3juihCSby0< at >public.gmane.org> wrote:

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